Please note this is a beta version of the Criteria Specification Registry. This resource is intended to provide access to Criteria Specifications used and applied by ClinGen Variant Curation Expert Panels and biocurators in the classification of variants.
For general information about ClinGen Expert Panels and Variant Curation please visit: Clinical Domain Working Groups. For specific inquiries regarding content correction or adding a new criteria specification refer to the Help page.
This resource is undergoing updates and testing. Should you encounter any issues regarding the data displayed, lack of functionality or other problems, please let us know by contacting us via email so we can rectify these accordingly. Your help in this regard is greatly appreciated.
Help
- Fill the Criteria Specification as mentioned in the template here.
- Once filled, send the template to brl-cspec at bcm dot edu
- The upcoming release of the Cspec Editor will allow VCEP coordinators and other members to directly add or change a Criteria Specification.
The Criteria Specifiication Registry provides RESTful-APIs to browse and search content. Responses are returned in JSON format.
Service URL: https://cspec.genome.network/cspec/
Several REST API endpoints are available to GET links and excerpts from CSpec. Detailed API documentation will be released soon.
Response from the API endpoints can be filtered or restricted using the following modifiers:
Modifiers | Possible values | Description | Example |
ids | Comma separated list of identifiers | Allows batch search of a list of identifiers | https://cspec.genome.network/cspec/SequenceVariantInterpretation/id?ids=GN014,GN016,GN015 |
types | Comma separated list of entity types | Allows filtering the results to show certain entity types only | https://cspec.genome.network/cspec/SequenceVariantInterpretation/id/GN016?types=Gene,RuleSet |
detail | low, med, high | low - Only identifier level info for the entity. The ld and ldFor just show the counts for 1+ such linked entity. med - (default) - The ld and ldFor show identifier level info. high - All details are shown. | https://cspec.genome.network/cspec/SequenceVariantInterpretation/id?detail=low https://cspec.genome.network/cspec/SequenceVariantInterpretation/id?detail=med https://cspec.genome.network/cspec/SequenceVariantInterpretation/id?detail=high |
fields | Coming soon (Full list of fields will be added in a separate section.) | Comma separated list of fields to get in the API response | https://cspec.genome.network/cspec/SequenceVariantInterpretation/id?detail=low&fields=entId,ldhId |
pg | Integer Default: 1 Min:1 | Page number to be retrieved | |
pgSize | Integer Default: 250 Min 1; Max: 250 | Number of results in each page |
The table below lists the key fields returned in the API response.
Key Fields | Description | Example |
ld | This entity is a linked data object for these entities | "ld": [ { "CriteriaCode": [ … ] }, {"RuleSet": [ … ] }, { "Gene": [ … ] } ], Here, "CriteriaCode", "RuleSet" and "Gene" are the linked data entities for the variant "CA000176" |
ldFor | This entity is linked data FOR these other entities | "ldFor": [ { "Gene": [ … ] } ], SequenceVariantInterpretation “CA000176” is linked data FOR the Gene “TP53” |
entId | Identifier of entity in the external data source | "entId": "GN016", where "GN016" - ClinGen Allele Registry identifier for “SequenceVariantInterpretation” |
entIri | IRI of entity in the external data source | "entIri": "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:1097", where the IRI is the “link” to this entity in the external data source |
entType | Type of entity | "entType": "SequenceVariantInterpretation", |
ldhId | CSpec identifier (Note: If data is embedded within CSpec, this will be the only identifier) | "ldhId": "41889804", |
ldhIri | CSpec IRI (Note: If data is embedded within CSpec, this will be the only IRI) | "ldhIri": "https://cspec.genome.network/cspec/SequenceVariantInterpretation/id/41889804" |
entContent | Excerpts from external data source | "entContent": {...} The excerpt content will be different for each entity type. Detailed documentation for the excerpt content stored for each type of entity will be added soon. |
modifier | Person who added this entity to CSpec | "modifier": "johndoe", |
modified | Modification timestamp value | "modified": "2019-10-03T17:04:35.395Z", |
The Criteria Specifiication Registry provides RESTful JSON-LD APIs to browse and search content. Responses are returned in JSON-LD format. Listed below are examples of JSON-LD API endpoints.
Service URL: https://cspec.genome.network/cspec/
Several REST JOSN-LD API endpoints are available to GET links and excerpts from CSpec. Detailed API documentation will be released soon.
Endpoints | Description | Example |
/api/context/{type} | Context to a specific entity type | https://cspec.genome.network/cspec/api/context/SequenceVariantInterpretation |
/api/{type}/id/{val} | Specific JSON-LD based identity-based lookup for an entity type | https://cspec.genome.network/cspec/api/SequenceVariantInterpretation/id/GN016 |
One Baylor Plaza, MS:BCM225 Suite 400D, Houston, TX, 77030
Questions or comments?